> Is there any sense to time at all in the output? What I mean is looking at
Yes, that is a schematic as a function of time (x-axis)...
> the output given below, does it mean that clusters 2 and 3 are the main
> clusters AFTER a  time when the structure is mostly close to cluster 1?
Initially the trajectory is in cluster zero and moves to cluster 1, then 
primarily swaps between 2 and 3 (with brief visits back to 1)
> #Cluster    0   6 ..
> #Cluster    1   3X9992  .X95       .                  .
> #Cluster    2       ....2 .365799652.59789898727886888767887666886
> #Cluster    3       .7997 ..342..34794.21.1.1272113111232112333113
                  time ----------->
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Received on Wed May 11 2011 - 12:00:04 PDT